Flooring (adjusting) values in Gene Expression Microarray data analysis?

Question

[mohammedtoufiq91]

Hi,

I am analysing large datasets in R, and came across an issue. There are some values less than 10 in the dataset and I would like to floor/adjust the values to (=10). I usually floor the values (=10) at the probe-level data > Normalize the data > then convert the data from probe-level to gene-level data by matching with Gene Symbols. I have a question, does adjusting operation makes sense for data at probe-level or gene-level? or do, you think it's OK at any level?

data.matrix[data.matrix<10]=10

Thank you,

Toufiq

[ATpoint]

Arbitrary altering data is usually not recommended. Be sure to follow standard pipelines such as outlined in the limma manual for microarrays.